Get accepted canonical names and taxonomy for a given species name

get_gbif_taxonomy(x, infraspecies = FALSE, fuzzy = TRUE, verbose = TRUE)

Arguments

x

a character string or vector of species names.

infraspecies

logical. If TRUE, the given name is resolved to infraspecies taxon, i.e. subspecies names will not be pooled (not working!)

fuzzy

logical. If TRUE, function tries fuzzy matching for species requests. May produce output, if normal matching fails. (not working!)

verbose

logical. If FALSE, warnings and messages are suppressed.

Value

a data.frame mapping the user supplied names to the accepted taxon names and higher taxonomic information (kingdom, phylum, class, order, family, genus).

Details

If 'synonym' is returned as TRUE, the user provided name has been identified as a synonym and was mapped to an accepted name. The field confidence reports the confidence of the matching procedure performed by the function 'get_gbifid_()' of the package 'taxize'. The taxonID is a globally valid URI that links to the taxon description of the GBIF backbone taxonomy.

Examples

get_gbif_taxonomy(c("Chorthippus albomarginatus", "Chorthippus apricarius", "Chorthippus biguttulus", "Chorthippus dorsatus", "Chorthippus montanus", "Chorthippus parallelus", "Chrysochraon dispar", "Conocephalus dorsalis", "Conocephalus fuscus", "Decticus verrucivorus", "Euthystira brachyptera", "Gomphocerippus rufus", "Gryllus campestris", "Metrioptera roeselii", "Omocestus viridulus", "Phaneroptera falcata", "Platycleis albopunctata", "Spec", "Stenobothrus lineatus", "Stenobothrus stigmaticus", "Stethophyma grossum", "Tetrix kraussi", "Tetrix subulata", "Tetrix tenuicornis", "Tetrix undulata", "Tettigonia cantans", "Tettigonia viridissima"))
#> #> Retrieving data for taxon 'Chorthippus albomarginatus'
#> #> Retrieving data for taxon 'Chorthippus apricarius'
#> #> Retrieving data for taxon 'Chorthippus biguttulus'
#> #> Retrieving data for taxon 'Chorthippus dorsatus'
#> #> Retrieving data for taxon 'Chorthippus montanus'
#> #> Retrieving data for taxon 'Pseudochorthippus montanus'
#> Warning: Synonym provided! Automatically set to accepted species Name!
#> #> Retrieving data for taxon 'Chorthippus parallelus'
#> #> Retrieving data for taxon 'Pseudochorthippus parallelus'
#> Warning: Synonym provided! Automatically set to accepted species Name!
#> #> Retrieving data for taxon 'Chrysochraon dispar'
#> #> Retrieving data for taxon 'Conocephalus dorsalis'
#> #> Retrieving data for taxon 'Conocephalus fuscus'
#> #> Retrieving data for taxon 'Decticus verrucivorus'
#> #> Retrieving data for taxon 'Euthystira brachyptera'
#> #> Retrieving data for taxon 'Gomphocerippus rufus'
#> #> Retrieving data for taxon 'Gryllus campestris'
#> #> Retrieving data for taxon 'Metrioptera roeselii'
#> #> Retrieving data for taxon 'Roeseliana roeselii'
#> Warning: Synonym provided! Automatically set to accepted species Name!
#> #> Retrieving data for taxon 'Omocestus viridulus'
#> #> Retrieving data for taxon 'Phaneroptera falcata'
#> #> Retrieving data for taxon 'Platycleis albopunctata'
#> #> Retrieving data for taxon 'Stenobothrus lineatus'
#> #> Retrieving data for taxon 'Stenobothrus stigmaticus'
#> #> Retrieving data for taxon 'Stethophyma grossum'
#> #> Retrieving data for taxon 'Tetrix kraussi'
#> #> Retrieving data for taxon 'Tetrix subulata'
#> #> Retrieving data for taxon 'Tetrix tenuicornis'
#> #> Retrieving data for taxon 'Tetrix undulata'
#> #> Retrieving data for taxon 'Tettigonia cantans'
#> #> Retrieving data for taxon 'Tettigonia viridissima'
#> scientificName synonym scientificNameStd #> 1 Chorthippus albomarginatus FALSE Chorthippus albomarginatus #> 2 Chorthippus apricarius FALSE Chorthippus apricarius #> 3 Chorthippus biguttulus FALSE Chorthippus biguttulus #> 4 Chorthippus dorsatus FALSE Chorthippus dorsatus #> 5 Pseudochorthippus montanus TRUE Pseudochorthippus montanus #> 6 Pseudochorthippus parallelus TRUE Pseudochorthippus parallelus #> 7 Chrysochraon dispar FALSE Chrysochraon dispar #> 8 Conocephalus dorsalis FALSE Conocephalus dorsalis #> 9 Conocephalus fuscus FALSE Conocephalus fuscus #> 10 Decticus verrucivorus FALSE Decticus verrucivorus #> 11 Euthystira brachyptera FALSE Euthystira brachyptera #> 12 Gomphocerippus rufus FALSE Gomphocerippus rufus #> 13 Gryllus campestris FALSE Gryllus campestris #> 14 Roeseliana roeselii TRUE Roeseliana roeselii #> 15 Omocestus viridulus FALSE Omocestus viridulus #> 16 Phaneroptera falcata FALSE Phaneroptera falcata #> 17 Platycleis albopunctata FALSE Platycleis albopunctata #> 18 <NA> NA <NA> #> 19 Stenobothrus lineatus FALSE Stenobothrus lineatus #> 20 Stenobothrus stigmaticus FALSE Stenobothrus stigmaticus #> 21 Stethophyma grossum FALSE Stethophyma grossum #> 22 Tetrix kraussi FALSE Tetrix kraussi #> 23 Tetrix subulata FALSE Tetrix subulata #> 24 Tetrix tenuicornis FALSE Tetrix tenuicornis #> 25 Tetrix undulata FALSE Tetrix undulata #> 26 Tettigonia cantans FALSE Tettigonia cantans #> 27 Tettigonia viridissima FALSE Tettigonia viridissima #> author taxonRank confidence kingdom phylum class #> 1 (De Geer, 1773) species 98 Animalia Arthropoda Insecta #> 2 (Linnaeus, 1758) species 98 Animalia Arthropoda Insecta #> 3 (Linnaeus, 1758) species 98 Animalia Arthropoda Insecta #> 4 (Zetterstedt, 1821) species 97 Animalia Arthropoda Insecta #> 5 (Charpentier, 1825) species 98 Animalia Arthropoda Insecta #> 6 (Zetterstedt, 1821) species 98 Animalia Arthropoda Insecta #> 7 (Germar, 1834) species 98 Animalia Arthropoda Insecta #> 8 (Latreille, 1804) species 98 Animalia Arthropoda Insecta #> 9 (Fabricius, 1793) species 98 Animalia Arthropoda Insecta #> 10 (Linnaeus, 1758) species 98 Animalia Arthropoda Insecta #> 11 (Ocskay, 1826) species 98 Animalia Arthropoda Insecta #> 12 (Linnaeus, 1758) species 98 Animalia Arthropoda Insecta #> 13 Linnaeus, 1758 species 97 Animalia Arthropoda Insecta #> 14 (Hagenbach, 1822) species 98 Animalia Arthropoda Insecta #> 15 (Linnaeus, 1758) species 98 Animalia Arthropoda Insecta #> 16 (Poda, 1761) species 98 Animalia Arthropoda Insecta #> 17 (Goeze, 1778) species 98 Animalia Arthropoda Insecta #> 18 <NA> <NA> NA <NA> <NA> <NA> #> 19 (Panzer, 1796) species 98 Animalia Arthropoda Insecta #> 20 (Rambur, 1838) species 98 Animalia Arthropoda Insecta #> 21 (Linnaeus, 1758) species 98 Animalia Arthropoda Insecta #> 22 Saulcy, 1888 species 97 Animalia Arthropoda Insecta #> 23 (Linnaeus, 1758) species 98 Animalia Arthropoda Insecta #> 24 (Sahlberg, 1891) species 98 Animalia Arthropoda Insecta #> 25 (Sowerby, 1806) species 98 Animalia Arthropoda Insecta #> 26 (Fuessly, 1775) species 97 Animalia Arthropoda Insecta #> 27 (Linnaeus, 1758) species 97 Animalia Arthropoda Insecta #> order family genus taxonomy #> 1 Orthoptera Acrididae Chorthippus GBIF Backbone Taxonomy #> 2 Orthoptera Acrididae Chorthippus GBIF Backbone Taxonomy #> 3 Orthoptera Acrididae Chorthippus GBIF Backbone Taxonomy #> 4 Orthoptera Acrididae Chorthippus GBIF Backbone Taxonomy #> 5 Orthoptera Acrididae Pseudochorthippus GBIF Backbone Taxonomy #> 6 Orthoptera Acrididae Pseudochorthippus GBIF Backbone Taxonomy #> 7 Orthoptera Acrididae Chrysochraon GBIF Backbone Taxonomy #> 8 Orthoptera Tettigoniidae Conocephalus GBIF Backbone Taxonomy #> 9 Orthoptera Tettigoniidae Conocephalus GBIF Backbone Taxonomy #> 10 Orthoptera Tettigoniidae Decticus GBIF Backbone Taxonomy #> 11 Orthoptera Acrididae Euthystira GBIF Backbone Taxonomy #> 12 Orthoptera Acrididae Gomphocerippus GBIF Backbone Taxonomy #> 13 Orthoptera Gryllidae Gryllus GBIF Backbone Taxonomy #> 14 Orthoptera Tettigoniidae Roeseliana GBIF Backbone Taxonomy #> 15 Orthoptera Acrididae Omocestus GBIF Backbone Taxonomy #> 16 Orthoptera Tettigoniidae Phaneroptera GBIF Backbone Taxonomy #> 17 Orthoptera Tettigoniidae Platycleis GBIF Backbone Taxonomy #> 18 <NA> <NA> <NA> <NA> #> 19 Orthoptera Acrididae Stenobothrus GBIF Backbone Taxonomy #> 20 Orthoptera Acrididae Stenobothrus GBIF Backbone Taxonomy #> 21 Orthoptera Acrididae Stethophyma GBIF Backbone Taxonomy #> 22 Orthoptera Tetrigidae Tetrix GBIF Backbone Taxonomy #> 23 Orthoptera Tetrigidae Tetrix GBIF Backbone Taxonomy #> 24 Orthoptera Tetrigidae Tetrix GBIF Backbone Taxonomy #> 25 Orthoptera Tetrigidae Tetrix GBIF Backbone Taxonomy #> 26 Orthoptera Tettigoniidae Tettigonia GBIF Backbone Taxonomy #> 27 Orthoptera Tettigoniidae Tettigonia GBIF Backbone Taxonomy #> taxonID #> 1 http://www.gbif.org/species/1708567 #> 2 http://www.gbif.org/species/1708601 #> 3 http://www.gbif.org/species/1708251 #> 4 http://www.gbif.org/species/8914202 #> 5 http://www.gbif.org/species/8423289 #> 6 http://www.gbif.org/species/7792296 #> 7 http://www.gbif.org/species/1700841 #> 8 http://www.gbif.org/species/1683331 #> 9 http://www.gbif.org/species/1683067 #> 10 http://www.gbif.org/species/1690685 #> 11 http://www.gbif.org/species/1701343 #> 12 http://www.gbif.org/species/1700023 #> 13 http://www.gbif.org/species/1716462 #> 14 http://www.gbif.org/species/4402879 #> 15 http://www.gbif.org/species/1710755 #> 16 http://www.gbif.org/species/1686243 #> 17 http://www.gbif.org/species/1685298 #> 18 <NA> #> 19 http://www.gbif.org/species/1710962 #> 20 http://www.gbif.org/species/1710986 #> 21 http://www.gbif.org/species/1711091 #> 22 http://www.gbif.org/species/9055856 #> 23 http://www.gbif.org/species/1681124 #> 24 http://www.gbif.org/species/1681181 #> 25 http://www.gbif.org/species/1681247 #> 26 http://www.gbif.org/species/8347376 #> 27 http://www.gbif.org/species/1692898 #> warnings #> 1 #> 2 #> 3 #> 4 #> 5 ; Synonym provided! Automatically set to accepted species Name! #> 6 ; Synonym provided! Automatically set to accepted species Name! #> 7 #> 8 #> 9 #> 10 #> 11 #> 12 #> 13 #> 14 ; Synonym provided! Automatically set to accepted species Name! #> 15 #> 16 #> 17 #> 18 ; No matching species name found! #> 19 #> 20 #> 21 #> 22 #> 23 #> 24 #> 25 #> 26 #> 27 #> user_supplied_name #> 1 <NA> #> 2 <NA> #> 3 <NA> #> 4 <NA> #> 5 Chorthippus montanus #> 6 Chorthippus parallelus #> 7 <NA> #> 8 <NA> #> 9 <NA> #> 10 <NA> #> 11 <NA> #> 12 <NA> #> 13 <NA> #> 14 Metrioptera roeselii #> 15 <NA> #> 16 <NA> #> 17 <NA> #> 18 Spec #> 19 <NA> #> 20 <NA> #> 21 <NA> #> 22 <NA> #> 23 <NA> #> 24 <NA> #> 25 <NA> #> 26 <NA> #> 27 <NA>